HI!

I have perform differential expression using DEXseq. We have this error:

> res1[res1$pvalue<0.05,]
Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :
  subscript contains NAs

 head(res1)

LRT p-value: full vs reduced

DataFrame with 6 rows and 10 columns
                             groupID   featureID exonBaseMean  dispersion         stat    pvalue
                         <character> <character>    <numeric>   <numeric>    <numeric> <numeric>
ENSG00000000003:E001 ENSG00000000003        E001     45.05291 0.024833508 9.440144e-01 0.3312476
ENSG00000000003:E002 ENSG00000000003        E002    167.46662 0.028307479 6.615706e-02 0.7970166
ENSG00000000003:E003 ENSG00000000003        E003    147.24603 0.029514694 5.911512e-06 0.9980601
ENSG00000000003:E004 ENSG00000000003        E004    111.41275 0.006392908 7.917571e-02 0.7784176
ENSG00000000003:E


R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.3 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=it_IT.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=it_IT.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=it_IT.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] DEXSeq_1.16.7              BiocParallel_1.4.3         pheatmap_1.0.8            
 [4] genefilter_1.52.0          rafalib_1.0.0              ggplot2_2.0.0             
 [7] limma_3.26.5               RColorBrewer_1.1-2         gplots_2.17.0             
[10] org.Hs.eg.db_3.2.3         RSQLite_1.0.0              DBI_0.3.1                 
[13] annotate_1.48.0            XML_3.98-1.3               AnnotationDbi_1.32.3      
[16] biomaRt_2.26.1             DESeq2_1.10.1              RcppArmadillo_0.6.400.2.2
[19] Rcpp_0.12.3                SummarizedExperiment_1.0.2 Biobase_2.30.0            
[22] GenomicRanges_1.22.3       GenomeInfoDb_1.6.1         IRanges_2.4.6             
[25] S4Vectors_0.8.7            BiocGenerics_0.16.1       

loaded via a namespace (and not attached):
 [1] statmod_1.4.23       gtools_3.5.0         locfit_1.5-9.1       splines_3.2.3       
 [5] lattice_0.20-33      colorspace_1.2-6     survival_2.38-3      foreign_0.8-66      
 [9] lambda.r_1.1.7       plyr_1.8.3           stringr_1.0.0        zlibbioc_1.16.0     
[13] Biostrings_2.38.3    munsell_0.4.2        gtable_0.1.2         futile.logger_1.4.1
[17] hwriter_1.3.2        caTools_1.17.1       labeling_0.3         latticeExtra_0.6-26
[21] geneplotter_1.48.0   acepack_1.3-3.3      KernSmooth_2.23-15   xtable_1.8-0        
[25] scales_0.3.0         gdata_2.17.0         Hmisc_3.17-1         XVector_0.10.0      
[29] Rsamtools_1.22.0     gridExtra_2.0.0      digest_0.6.9         stringi_1.0-1       
[33] grid_3.2.3           tools_3.2.3          bitops_1.0-6         magrittr_1.5        
[37] RCurl_1.95-4.7       Formula_1.2-1        cluster_2.0.3        futile.options_1.0.0
[41] rpart_4.1-10         nnet_7.3-11 

The vector you are using to subscript, res1$pvalue<0.05, contains NA's, and it does not make sense to subscript a data frame with NA indexes (base R's data.frame inserts a row with all NA, Bioconductor's DataFrame issues the complaint you see). Replace NA's with FALSE, e.g., with res1[!is.na(res1$pvalue) & (res1$pvalue < 0.05),].

Thanks so much!!

Now I  have this error:

mp<-res1[!is.na(res1$pvalue) & (res$pvalue < 0.05),]
Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :
  subscript contains NAs
In addition: Warning message:
In !is.na(res1$pvalue) & (res$pvalue < 0.05) :
  longer object length is not a multiple of shorter object length